[ensembl-dev] HGMD-PUBLIC records in Variation

Laurent Gil lgil at ebi.ac.uk
Mon Jul 11 10:57:57 BST 2011


Hi,

The Ensembl API allows us to map the coordinates between different 
assemblies.
So we just remap the NCBI36 positions to the GRCh37 before import them 
in the Ensembl Variation database.

Cheers,

Laurent


On 08/07/2011 13:42, Sung Gong wrote:
> Hi,
>
> I found the HGMD is built on gene build 36.3.
> Just wondered how you mapped HGMD entries onto Ensembl?
> I presume that blast after lifting-over?
>
> Cheers,
> Sung
>
> On 24 May 2011 16:37, Fiona Cunningham<fiona at ebi.ac.uk>  wrote:
>>   Hello,
>>
>> HGMD does not release their alleles to us as this information is not
>> publicly available. This means we can only display the location of the
>> data and type of variation but unfortunately no alleles and no
>> consequences. If you have a subscription to HGMD  you can click
>> through the allele data on the HGMD website from the link on the
>> ensembl website.
>>
>> Best regards,
>>
>> Fiona
>>
>> ------------------------------------------------------
>> Fiona Cunningham
>> Ensembl Variation Project Leader, EBI
>> www.ensembl.org
>> www.lrg-sequence.org
>> t: 01223 494612 || e: fiona at ebi.ac.uk
>>
>>
>>
>> On 24 May 2011 16:30, Sung Gong<sung at bio.cc>  wrote:
>>> Hi all,
>>>
>>> Not vigorously tested yet, but some HGMD identifiers (e.g CM043264)
>>> does not have any 'allele_string' in their variation feature object:
>>>
>>> my $v=$va->fetch_by_name('CM043264');
>>>
>>> foreach my $vf (@{$vfa->fetch_all_by_Variation($v)}) {
>>>     print $vf->variation_name(), ":", $vf->allele_string(),"\n";
>>>     print $vf->seq_region_name,":", $vf->seq_region_start,
>>> '-',$vf->seq_region_end,"\n";
>>> }
>>>
>>> The script above returns:
>>> CM043264:HGMD_MUTATION
>>> 3:8775661-8775661
>>>
>>> Can anyone explain how the HGMD-public data is incorporated into
>>> Ensembl human variation?
>>>
>>> Cheers,
>>> Sung
>>>
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